Align PEP-dependent dihydroxyacetone kinase 2, ADP-binding subunit DhaL; EC 2.7.1.121 (characterized)
to candidate 3607104 Dshi_0526 Dak phosphatase (RefSeq)
Query= SwissProt::Q92EU3 (216 letters) >FitnessBrowser__Dino:3607104 Length = 199 Score = 75.5 bits (184), Expect = 7e-19 Identities = 52/180 (28%), Positives = 85/180 (47%), Gaps = 9/180 (5%) Query: 18 MGALIEKERDYLTGLDSDIGDGDHGINLSIGFREVNKQLDELLTVSPDIATLLKKSGMIL 77 + A +E++ D L D+ +GDGD G+ ++ G R + D+L DI L Sbjct: 15 IAAAMERDFDLLNSADAALGDGDLGVTMTRGMRAIVAMKDDL---PEDIGMALLGCAQAF 71 Query: 78 LGKVGGASGPLYGSFFMKCGADVPGKTEVNFDELCGMIINGAAAVQHRGKAELGDKTMMD 137 G + G L + M ++ G+ E+ + + G+I +Q RGKAELG KT++D Sbjct: 72 TKSSGSSYGTLMATGLMSAAKELRGQQEIESESIPGLIAGARDKMQERGKAELGGKTVLD 131 Query: 138 AFLPGVEVLQNRDTNADPIETFSAFVDAMHAGAQSTIPLIAKKGRALRLGERAIGHLDPG 197 + ++ + AD + SA +A+ + A GRA GE++IG DPG Sbjct: 132 S----LDYVARTTDKAD--DKASAAAEAVDRALEDFRDKPATVGRARIFGEKSIGLDDPG 185 Lambda K H 0.318 0.138 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 107 Number of extensions: 6 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 216 Length of database: 199 Length adjustment: 21 Effective length of query: 195 Effective length of database: 178 Effective search space: 34710 Effective search space used: 34710 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory